v1.0.0-rc.166 (#76)

* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.

Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

image_analysis/spot_finding/SpotUtils.cpp

@@ -129,7 +129,7 @@ namespace {
     constexpr size_t SPOT_RESOLUTION_MIN_SPOTS = 4;
 }
 
-std::optional<float> GetResolution(const std::vector<SpotToSave> &spots, float detector_d_min_A) {
+std::optional<float> GetResolution(const std::vector<SpotToSave> &spots) {
     // Each spot enters weighted by its own signal-to-noise. The intensity is a summed photon count, so
     // it is Poisson and its significance is sqrt(I): that keeps a marginal high-resolution detection
     // from counting for as much as a real reflection, without letting the handful of very strong
@@ -161,10 +161,10 @@ std::optional<float> GetResolution(const std::vector<SpotToSave> &spots, float d
             break;
     }
 
-    const float d_A = 1.0f / (SPOT_RESOLUTION_MERGE_REACH * std::sqrt(one_over_d2));
-
-    // However far the crystal diffracts, no merge reaches past the corner of the detector.
-    return detector_d_min_A > 0.0f ? std::max(d_A, detector_d_min_A) : d_A;
+    // Not clamped at the corner of the detector. The quantile is read from the middle of the
+    // fall-off, so it still measures the crystal where the detector cuts that fall-off short;
+    // clamping reported where the detector stops instead, which is the one thing this is not for.
+    return 1.0f / (SPOT_RESOLUTION_MERGE_REACH * std::sqrt(one_over_d2));
 }
 
 void GenerateSpotPlot(DataMessage &msg, const std::vector<SpotToSave> &spots, float d_min_A) {
@@ -232,7 +232,7 @@ void SpotAnalyze(const DiffractionExperiment &experiment,
     GenerateSpotPlot(output, spots_out,
                      spot_d_min.value_or(0.0f) > 0 ? *spot_d_min : experiment.GetDetectorMaxResolution_A());
 
-    output.resolution_estimate = GetResolution(spots_out, experiment.GetDetectorMaxResolution_A());
+    output.resolution_estimate = GetResolution(spots_out);
 
     // One decision drives both: if indexing is to use the ice-band spots, the spot budget must not
     // throw them away before it gets the chance.